Often in these case you actually don't need to represent areas that are vertically above each other at the same time at all.
Not always, but often.
These days I mostly use theater-of-the-mind, with maybe a few sketches to show building layout, which of course avoids the problem altogether.
But based on what I learned from when I was using battle-maps, it is worth remembering what the map is actually giving you.
It gives you precise locations for purposes of knowing about the PCs:
- Movement range, so you know how many turns it takes to get somewhere
- tactical maneuvers like attacks of opportunity and flanking
- weapon ranges
- situational awareness of enemy locations
Notice that I bold the PCs; there is no need to represent stuff about NPC-NPC interaction on the map; since precise information about it will not be known to the PCs except as the last point.
So with that known, you can avoid showing some locations on the map and draw from what we do in the theater of the mind world. Descriptions.
You can describe things like "You can hear what sounds like maybe 5 or 6 guards strapping on armour and cussing inside the gate house. Might only be 3 but if so they are loud."
To illustrate with some examples.
An outpost with a guard tower with archers on the top floor and melee fighters guarding the door on the ground floor. Both the archers on the top floor and the fighters on the bottom floor can attack the same monsters approaching the outpost.
Until monsters get inside the walls, you never need to show the melee fighters being below the archers -- if they are engaging with the monsters are the same time as the archers then they must be in-front of the wall (the archers can not shoot directly down through there floor/roof)
Then once the monsters are inside the walls, you don't need to represent the archers on the outside at all anymore. Just draw the inside of the fortification -- remembering to include the stairs and ladders where the archers will emerge.
An adventurers’ ship is being attacked by a kraken. Fighters and wizards on deck attack it while crew members below deck operate cannons or the like.
Here we don't need to represent below deck at all.
If a PC is operating the cannons below deck, just don't show the below-deck area at all.
To address the issues from before:
- Movement range: Just tell them it will take (say) 1 full turn of movement to get on deck. (Or give it in units of squares if you must.)
- Tactical maneuvers: There are no melee combatants below deck, so this is fine; and below deck, they are probably safe from all attack. If they are attacked, it isn't really tactical so much as a single event (e.g. "The kraken grabs the cannon and swings it around before ripping it out. Roll Dodge or take X damage"), so a description works better than a mat here anyway.
- Weapon ranges: The range on a cannon is going to be enough - or it isn't. It isn't like you can maneuver to change it much.
- Situational awareness of enemy locations: The kraken's location is shown on the overhead map, and that is all that really matters.
Obviously if you have to show two locations, you have to show two locations.
I think this is in general a much harder issue with flying characters than it is for multiple floors, since you can't interact through most floors.